metacoder (version 0.3.7)

stems: Get stem taxa

Description

Return the stem taxa for a [taxonomy()] or a [taxmap()] object. Stem taxa are all those from the roots to the first taxon with more than one subtaxon.

obj$stems(subset = NULL, simplify = FALSE,
  value = "taxon_indexes", exclude_leaves = FALSE)
stems(obj, subset = NULL, simplify = FALSE,
  value = "taxon_indexes", exclude_leaves = FALSE)

Value

`character`

Arguments

obj

The [taxonomy()] or [taxmap()] object containing taxon information to be queried.

subset

Taxon IDs, TRUE/FALSE vector, or taxon indexes to find stems for. Default: All taxa in `obj` will be used. Any variable name that appears in [all_names()] can be used as if it was a vector on its own.

value

What data to return. This is usually the name of column in a table in `obj$data`. Any result of `all_names(obj)` can be used, but it usually only makes sense to data that corresponds to taxa 1:1, such as [taxon_ranks()]. By default, taxon indexes are returned.

simplify

(`logical`) If `TRUE`, then combine all the results into a single vector of unique values.

exclude_leaves

(`logical`) If `TRUE`, the do not include taxa with no subtaxa.

See Also

Other taxonomy indexing functions: branches(), internodes(), leaves(), roots(), subtaxa(), supertaxa()

Examples

# Return indexes of stem taxa
stems(ex_taxmap)

# Return indexes for a subset of taxa
stems(ex_taxmap, subset = 2:17)

# Return something besides taxon indexes
stems(ex_taxmap, value = "taxon_names")

# Return a vector instead of a list
stems(ex_taxmap, value = "taxon_names", simplify = TRUE)